Utility of Whole Genome Amplification (WGA) To Enable Virtual Karyotyping with SNP Arrays in Paraffin-Embedded Brain Tumor Biopsies with Limited Tissue
Sergio Pina-Oviedo, Karla Alvarez, Suzanne Z Powell, Chung C (Jeff) Chang, Federico A Monzon. The Methodist Hospital, Houston, TX
Background: Virtual karyotyping with SNP (single nucleotide polymorphism) arrays has been established as a novel and reliable diagnostic tool for several types of tumors, including brain tumors. Specific molecular alterations have been linked to central nervous system (CNS) neoplasms, such as co-deletion of 1p19q in oligodendrogliomas and overexpression of EGFR in glioblastomas. Frequently, very small samples are obtained from brain biopsies and the limited amount of tissue may limit the ability to obtain an accurate diagnosis. We evaluated the use of whole genome amplification (WGA) in order to perform virtual karyotyping in paraffin-embedded brain tissue biopsies.
Design: DNA was extracted from microdissected tissue from paraffin-embedded blocks in three cases of oligodendrogliomas and one case of glioblastoma that were confirmed by morphology and evaluated for 1p/19q deletions by fluorescence in-situ hybridization (FISH). WGA of extracted DNA was performed using the RepliG FFPE kit (Qiagen) with manufacturer's recommendation and with a modified protocol. Virtual karyotyping was then performed on these samples using Affymetrix 250K Nsp SNP arrays. Additional tumor samples from other tissue types were also evaluated to evaluate the reliability of the method.
Results: By using WGA with SNP arrays we were able to confirm the presence of 1p19q co-deletion starting from 50ng of DNA from the anaplastic oligodendroglioma and glioma samples. In addition, characteristic chromosomal imbalances were identified in the glioblastoma including amplification of EGFR. Our results correlated with the results obtained from FISH in all cases. The WGA method was successfully applied to samples from kidney and bone marrow specimens.
Conclusions: We demonstrate that whole genome molecular analysis tools can be used in samples with limited amount of tissue by using WGA and SNP cytogenomic arrays. Our data demonstrates that WGA can be potentially used as a diagnostic tool in small samples, especially those where diagnosis cannot be established on routine grounds but further testing is hampered by the limited amount of tissue. Although the efficacy our WGA approach was of 100% of the cases, larger series are necessary to confirm the reliability of this method. This technique should be of practical use in neuropathology, since frequently CNS biopsies are small and molecular analysis are increasingly used to confirm diagnoses and for selection of therapy.
Tuesday, March 20, 2012 1:00 PM
Poster Session IV # 273, Tuesday Afternoon